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7d7b2c2
initial test commit
May 29, 2018
e96e620
Update Fitclasses.py
lillian542 May 29, 2018
55c2081
converter for legacy and SQL data to dictionary, fitter to find fit f…
lillian542 Jun 5, 2018
d07832e
Remove out of date comment
lillian542 Jun 6, 2018
b57eacf
Merge remote-tracking branch 'lillian/fitter_extension' into fitter_e…
lillian542 Jun 6, 2018
7b6bd3a
Readd file removed somehow
lillian542 Jun 6, 2018
0354584
fixing location to import from
lillian542 Jun 6, 2018
e2387ad
add cut direction to fit metadata
lillian542 Jun 6, 2018
4472120
renaming metadata for legacy converter to match pattern of SQL converter
lillian542 Jun 6, 2018
86f8b24
takes data + fit, dictionaries, saves as new SQL dataset
lillian542 Jun 6, 2018
135fcd9
Create umbreall function for conversion to dict
lillian542 Jun 7, 2018
f217dae
add units to parameters in fit
lillian542 Jun 7, 2018
e65b217
fix bug when manually specifying axes for 1D data
lillian542 Jun 7, 2018
c54ad41
Add plotting from fit and data dictionaries
lillian542 Jun 7, 2018
f533b2e
Remove typo
lillian542 Jun 7, 2018
7cdf83d
Add numbering to tables if identical table names are created
lillian542 Jun 25, 2018
88528e1
Fix bug - add missing SQL cursor in table functions
lillian542 Jun 25, 2018
d7a996c
Fix bug in table name that inserts data into incorrect table
lillian542 Jun 25, 2018
c265ad2
Remove redundancies between data and analysis tables
lillian542 Jun 25, 2018
00c1464
Print confirmation after table creation
lillian542 Jun 25, 2018
b0d59a1
Store metadata about data location and analysis in SQL database
lillian542 Jun 25, 2018
02c1d18
Create Jupyter notebook example document for fitter
lillian542 Jun 26, 2018
7e09565
Fix bug reversing units in vertical-cut 2D fits
lillian542 Jun 26, 2018
8b90524
Remove long and unnecessary outputs from Example notebook
lillian542 Jun 26, 2018
5a51be8
Fix bug in setting 1D plot units
lillian542 Jun 26, 2018
73e7092
Fix bug I made fixing last bug
lillian542 Jun 26, 2018
27b8a19
Update Example notebook after bug fixes
lillian542 Jun 26, 2018
c0774c4
Change variable name from data_id to run_id
lillian542 Jun 27, 2018
8c5a267
Add dill of fitclass to fit dictionary
lillian542 Jun 27, 2018
bb2cc9b
Change Fitter from class to function
lillian542 Jun 27, 2018
357dc3d
Remove default_dependencies option, require user to specify explicitly
lillian542 Jun 27, 2018
765c750
Update Example notebook to reflect changes
lillian542 Jun 27, 2018
1394cca
Rename fit function to avoid confusion between function and its result
lillian542 Jun 27, 2018
7260652
Remove unnecessary header from Example notebook
lillian542 Jun 27, 2018
d7c0df1
Add initial guess for parameters to fit dictionary
lillian542 Jun 27, 2018
506f3dd
Add function fitted to fit dictionary metadata
lillian542 Jun 27, 2018
f7c472e
Remove overlooked remnants of default_dependencies
lillian542 Jun 27, 2018
1c50681
Put analysis data in experiments.db instead of separate file.
lillian542 Jun 27, 2018
d3c98b4
Move calculation of estimated function output from SQL conversion to …
lillian542 Jun 28, 2018
02dd660
Add fun_vars attribute to fitclasses - list of variables function takes
lillian542 Jun 28, 2018
384fff7
Change fitter back to class
lillian542 Jun 28, 2018
720040b
Modify fitter to use function based rather than graphic/visualization…
lillian542 Jun 30, 2018
352b736
Add guess parameters to SQL database
lillian542 Jul 10, 2018
2d798f3
Add dill of fitter to SQL (previously only contained fitclass
lillian542 Jul 10, 2018
f79b2d0
Throw error if count in is_table does not return 1 or 0.
lillian542 Jul 17, 2018
cc9375a
Fix while... else statement
lillian542 Jul 17, 2018
f7d51e1
Organize document and add comments for ease of reading
lillian542 Jul 17, 2018
2072321
Remove hard coded database name
lillian542 Jul 17, 2018
7c918ac
Add clarifying comment about the new database argument
lillian542 Jul 17, 2018
ee64f56
Define functions with NotImplementedError in base class, add comments
lillian542 Jul 17, 2018
a17cb58
Throw error if SQL converter find_data method does not find data
lillian542 Jul 17, 2018
676a821
Make it possible to get database from qc.config
lillian542 Jul 17, 2018
f55d723
Remove hard coded database name, replace with qc.config retrieval of …
lillian542 Jul 17, 2018
d93753b
Add manual specification of sample folder to find_experiment and find…
lillian542 Jul 17, 2018
f7c992b
Fix bug created by addition of manual samplefolder specification.
lillian542 Jul 18, 2018
edfcd3d
Tidy document up
lillian542 Jul 18, 2018
79b5f69
Add 'fun' and 'guess' functions with NotImplementedError in base class
lillian542 Jul 18, 2018
ddb3290
Add docstring to Fitclasses
lillian542 Jul 18, 2018
a12750b
Reorganize Fitter as parent and child classes
lillian542 Jul 18, 2018
96f29a7
Add description to Fitter class
lillian542 Jul 18, 2018
ec1c358
Update Example notebook to reflect changes
lillian542 Jul 18, 2018
98ef6d1
Remove unnecessary printing of data from Example notebook
lillian542 Jul 18, 2018
a5df7bf
Move function checking for correct inputs out of Fitter class
lillian542 Jul 19, 2018
eab25c6
Fix references to fit dicionary to reflect fit dict restructuring
lillian542 Jul 19, 2018
4112f24
Update explanatory text in Example doc to reflect changes
lillian542 Jul 19, 2018
5dbdb4b
Add clarifying comments to rough plotting functions
lillian542 Jul 19, 2018
ea61e89
Clean up Fitter and add explanatory comments
lillian542 Jul 19, 2018
cab0b62
pep8 and comments updated, Fitclasses to have more generic names and …
nataliejpg Aug 16, 2018
3abe329
remove samplefolder concept from converter, converter now assumes tha…
nataliejpg Aug 16, 2018
a0cf79b
id -> run_id everywhere
nataliejpg Aug 16, 2018
22de21a
restructure fit_to_sql into two functions, one creates named_tuple of…
nataliejpg Aug 16, 2018
9a2579b
update docstrings
nataliejpg Aug 16, 2018
918ab59
rename converter and data saver files to better represent their funct…
nataliejpg Aug 16, 2018
43000ef
rename key functions for data extraction and fit saving
nataliejpg Aug 16, 2018
cc7e053
fix duplicate naming bug I just introduced to fit_saving file and mak…
nataliejpg Aug 16, 2018
3c80e44
rename Fitclasses
nataliejpg Aug 16, 2018
0569bb3
rewrite fitter to do 1 dimensional fits for any number of setpoints a…
nataliejpg Aug 22, 2018
9bfe645
rewrite least suares to recognise that only 1d fits are supported and…
nataliejpg Aug 22, 2018
c09c527
add logic for saving fits
nataliejpg Aug 28, 2018
d523c37
make it possible to specify guess params for fit
nataliejpg Aug 28, 2018
8b77a66
measuring on t2 edits
nataliejpg Sep 4, 2018
1cdfa42
Merge pull request #1 from nataliejpg/fitter_extension
lillian542 Sep 5, 2018
d164ef8
Add 1d plotting to fitter
lillian542 Sep 11, 2018
6f755f7
2D heat map fit plots, error bars on plots, R2 fitting threshhold and…
lillian542 Sep 18, 2018
724ef5f
file name changing part 1
lillian542 Sep 18, 2018
46d8e02
file name changing part 2
lillian542 Sep 18, 2018
4409a8f
fit from run id
nataliejpg Sep 24, 2018
a6c80a4
Add perform_fit function to fitclass
lillian542 Sep 25, 2018
55abebb
Fix merge conflict
lillian542 Sep 25, 2018
0cb1c74
Add missing func to ExpDexaySin
lillian542 Sep 25, 2018
713a396
Merge branch 'master' into dismantling_fitter
lillian542 Sep 25, 2018
ef4e7f8
Transferring stuff from QInfer notebook
lillian542 Sep 25, 2018
360fc81
Use ordered dictionary to define parameter info in __init__
lillian542 Sep 25, 2018
96a398c
reorganization into fitter, guesses and models
lillian542 Sep 27, 2018
ff9579c
Correct T2 to T1 in class names
lillian542 Sep 27, 2018
37359f8
Update RabiT1 model to include second term in equation
lillian542 Sep 27, 2018
bdd5586
Add rough plotting from analysis instrument and dataset
lillian542 Sep 27, 2018
28dff4e
plot saving to be specified in config.user
nataliejpg Dec 5, 2018
af2bf27
make requirement for config.user section to be flatter
nataliejpg Dec 5, 2018
d47932b
remove plottr import from doNd example notebook
nataliejpg Dec 5, 2018
4eaa5c8
Restructure and change many things
lillian542 Jan 21, 2019
29020fe
Change fit saving to stop cutting off text box displaying fit parameters
lillian542 Feb 12, 2019
7a4a501
Didn't mean to add those
lillian542 Feb 12, 2019
08cfb21
Change analysis dataset name from analysis to results
lillian542 Feb 12, 2019
8d594da
Add parameters dictionary to minimum model for plotting
lillian542 Feb 19, 2019
42aa83d
Move error message affecting only 1d plotting to 1d plotting function
lillian542 Feb 19, 2019
432cc29
Fix typo
lillian542 Feb 27, 2019
db55a92
Fix import statements
lillian542 Mar 15, 2019
57d4db7
WIP reorganising fitter
nataliejpg Apr 8, 2019
000a399
make save_image more flexible so that it can be used outside of the d…
nataliejpg Apr 8, 2019
5cbebbb
fix bugs where old private function name used and name extension adde…
nataliejpg Apr 8, 2019
26024f0
Merge branch 'master' into plot_saving_to_config
nataliejpg Apr 8, 2019
497306c
Merge branch 'plot_saving_to_config' into dismantling_fitter
nataliejpg Apr 8, 2019
66679ce
change kwarg experiment_name to shorter (and used elsewhere) exp_name…
nataliejpg Apr 9, 2019
0716fdd
Merge branch 'plot_saving_to_config' into dismantling_fitter
nataliejpg Apr 9, 2019
75c95a7
rewritted to use load_by_id instead of get_data_by_id and works to fi…
nataliejpg Apr 9, 2019
5b2c76d
fitting cleaned up and tested and examples added. also adds a databas…
nataliejpg Apr 11, 2019
110ba72
removing any fit datasets from the transmons.db, should add to gitign…
nataliejpg Apr 11, 2019
c583ec9
docstrings and small cosmetic changes
nataliejpg Apr 13, 2019
25f38d1
resetting doND example to master version
nataliejpg Apr 13, 2019
1103d53
run example notebook to check i didnt break anything and make plottr …
nataliejpg Apr 13, 2019
3120c7b
Merge branch 'plot_saving_to_config' into dismantling_fitter
nataliejpg Apr 13, 2019
beff185
hacky solution to circumvent new db stucture: doesnt work for 2d plot…
nataliejpg Sep 17, 2019
77679e0
update data extraction to work with new data storing
nataliejpg Sep 19, 2019
2dba960
allow loading from one database and saving to another
nataliejpg Jan 28, 2020
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2 changes: 1 addition & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -40,4 +40,4 @@ tmp/
.idea

# qcodes
experiments.db
*.db
71 changes: 41 additions & 30 deletions examples/dataset/Example of doND wrappers.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 25,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -24,7 +24,10 @@
"from qcodes.dataset.database import initialise_database\n",
"from qcodes.dataset.experiment_container import new_experiment\n",
"from qcodes.dataset.plotting import plot_by_id\n",
"import plottr\n",
"try:\n",
" import plottr\n",
"except ModuleNotFoundError:\n",
" pass\n",
"import qcodes.config\n",
"from qcodes.tests.instrument_mocks import DummyChannelInstrument"
]
Expand All @@ -46,17 +49,25 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Upgrading database: : 0it [00:00, ?it/s]\n",
"Upgrading database: : 0it [00:00, ?it/s]\n"
]
},
{
"data": {
"text/plain": [
"doNd-tutorial#no sample#10@C:\\Users\\jenielse/experiments.db\n",
"-----------------------------------------------------------"
"doNd-tutorial#no sample#1@/Users/natalie/experiments.db\n",
"-------------------------------------------------------"
]
},
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -68,7 +79,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -81,7 +92,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -100,7 +111,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -120,15 +131,15 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Starting experimental run with id: 27\n",
"plot by id took 0.19638419151306152\n"
"Starting experimental run with id: 1\n",
"plot by id took 0.037342071533203125\n"
]
}
],
Expand All @@ -138,7 +149,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 9,
"metadata": {
"scrolled": false
},
Expand All @@ -147,8 +158,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"Starting experimental run with id: 28\n",
"plot by id took 1.528921365737915\n"
"Starting experimental run with id: 2\n",
"plot by id took 0.3784291744232178\n"
]
}
],
Expand All @@ -175,7 +186,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -197,15 +208,15 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 16,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"called before the loop\n",
"Starting experimental run with id: 29\n",
"Starting experimental run with id: 6\n",
"called at each step\n",
"called at each step\n",
"called at each step\n",
Expand All @@ -217,7 +228,7 @@
"called at each step\n",
"called at each step\n",
"called after the loop\n",
"plot by id took 0.1400294303894043\n"
"plot by id took 0.03285670280456543\n"
]
}
],
Expand All @@ -228,15 +239,15 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 17,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"called before the loop\n",
"Starting experimental run with id: 30\n",
"Starting experimental run with id: 7\n",
"called before inner loop\n",
"called at each step\n",
"called at each step\n",
Expand All @@ -250,7 +261,7 @@
"called at each step\n",
"called after inner loop\n",
"called after the loop\n",
"plot by id took 0.18652963638305664\n"
"plot by id took 0.06169295310974121\n"
]
}
],
Expand All @@ -272,7 +283,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -281,15 +292,15 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 19,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Starting experimental run with id: 31\n",
"plot by id took 0.15599322319030762\n"
"Starting experimental run with id: 8\n",
"plot by id took 0.03528785705566406\n"
]
}
],
Expand Down Expand Up @@ -328,7 +339,7 @@
},
{
"cell_type": "code",
"execution_count": 22,
"execution_count": 20,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -337,15 +348,15 @@
},
{
"cell_type": "code",
"execution_count": 23,
"execution_count": 21,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Starting experimental run with id: 35\n",
"plot by id took 0.07499814033508301\n"
"Starting experimental run with id: 9\n",
"plot by id took 0.045063018798828125\n"
]
}
],
Expand Down
297 changes: 297 additions & 0 deletions examples/fitting/DIY Fitting.ipynb

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